If i've read this properly, you already had fish in your tank which i assume was cycled??. If so there's no need to use old tank water, you can use fresh, treated of course!!. It's your filter were most of your bb is stored. You don't need to throw away your used filter pads because they're full of gunk. Just rinse them in used tank water..Filter pads have a very long life. I'm not saying not to follow the manufacturers instructions, but think about it, who's selling the replacements that you don't really need $$$. It is good bacteria that live even in gunky pads. Your just basically throwing away good bacteria..
BB(beneficial bacteria) only exist in the water in tiny amounts, it lives in your filter, glass, decor and substrate. You will be fine just swapping out you gravel for sand..
Make sure you wash the sand really, really, really well. Put some in a large bucket and use a garden hose to stir it up. Tilt the bucket and wash until the water runs clear. Then do it again..Washing it really well outside the tank, will stop it cloudy. It'll also get rid of dirt and light floaty sand. This is what clouds the tank. Also that floaty sand will get into your filter and not do it any favours...
If your putting the sand in the tank with water already in it(easier just to drain it??), get a piece of tube/pipe and place the tube/pipe in the water were you want the sand and simply pour the sand into the tube/pipe...